Here’s a list of some other notable organizations using MU. I’ll be updating this as I learn more links to high profile multisites.

The presentation at WordCamp suggested that New York Times Blogs and Ryerson University also are, but I can’t find evidence of this. I’ve asked the presenters.
Update! @andrea_r tells me that http://rsatechnologies.in/hide-wordpress-info-from-source-code.html hides the WordPress signatures from the code. Good for security!